Package evaluation of PhyNEST on Julia 1.13.0-DEV.971 (04e26c5eae*) started at 2025-08-11T03:31:22.979 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.15s ################################################################################ # Installation # Installing PhyNEST... Resolving package versions... Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Libuuid_jll ───────────────── v2.41.0+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed Libtiff_jll ───────────────── v4.7.1+0 Installed InlineStrings ─────────────── v1.4.4 Installed Optim ─────────────────────── v1.13.2 Installed Functors ──────────────────── v0.3.0 Installed Xorg_libXinerama_jll ──────── v1.1.6+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed OrderedCollections ────────── v1.8.1 Installed Fontconfig_jll ────────────── v2.16.0+0 Installed SentinelArrays ────────────── v1.4.8 Installed Wayland_protocols_jll ─────── v1.44.0+0 Installed FileIO ────────────────────── v1.17.0 Installed libsass_jll ───────────────── v3.6.6+0 Installed NaNMath ───────────────────── v1.1.3 Installed Librsvg_jll ───────────────── v2.54.7+0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Graphics ──────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed Tables ────────────────────── v1.12.1 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed LZO_jll ───────────────────── v2.10.3+0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed NLSolversBase ─────────────── v7.10.0 Installed Missings ──────────────────── v1.2.0 Installed Reexport ──────────────────── v1.2.2 Installed Preferences ───────────────── v1.4.3 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed EpollShim_jll ─────────────── v0.0.20230411+1 Installed Crayons ───────────────────── v4.1.1 Installed UnPack ────────────────────── v1.0.2 Installed ADTypes ───────────────────── v1.16.0 Installed SortingAlgorithms ─────────── v1.2.2 Installed MacroTools ────────────────── v0.5.16 Installed DiffResults ───────────────── v1.1.0 Installed FillArrays ────────────────── v1.13.0 Installed DataStructures ────────────── v0.18.22 Installed AbstractTrees ─────────────── v0.4.5 Installed OpenSSH_jll ───────────────── v9.9.2+0 Installed Sass ──────────────────────── v0.2.0 Installed Xorg_libXdamage_jll ───────── v1.1.6+0 Installed DelimitedFiles ────────────── v1.9.1 Installed CodecZlib ─────────────────── v0.7.8 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Cairo ─────────────────────── v1.1.1 Installed Observables ───────────────── v0.5.5 Installed ArrayInterface ────────────── v7.19.0 Installed StatsBase ─────────────────── v0.33.21 Installed MethodAnalysis ────────────── v0.4.13 Installed Xorg_libXfixes_jll ────────── v6.0.1+0 Installed DataValueInterfaces ───────── v1.0.0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed CEnum ─────────────────────── v0.5.0 Installed CommonSubexpressions ──────── v0.3.1 Installed RoundingIntegers ──────────── v1.1.0 Installed Expat_jll ─────────────────── v2.6.5+0 Installed IrrationalConstants ───────── v0.2.4 Installed Xorg_libXcursor_jll ───────── v1.2.4+0 Installed libpng_jll ────────────────── v1.6.50+0 Installed BitFlags ──────────────────── v0.1.9 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed Scratch ───────────────────── v1.3.0 Installed PDMats ────────────────────── v0.11.35 Installed Setfield ──────────────────── v1.1.2 Installed PooledArrays ──────────────── v1.4.3 Installed IOCapture ─────────────────── v0.2.5 Installed BenchmarkTools ────────────── v1.6.0 Installed FASTX ─────────────────────── v2.1.7 Installed GTK4_jll ──────────────────── v4.18.6+0 Installed WorkerUtilities ───────────── v1.6.1 Installed DocStringExtensions ───────── v0.9.5 Installed ForwardDiff ───────────────── v1.0.1 Installed Graphene_jll ──────────────── v1.10.8+0 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed AliasTables ───────────────── v1.1.3 Installed adwaita_icon_theme_jll ────── v43.0.1+0 Installed StringViews ───────────────── v1.3.5 Installed ShiftedArrays ─────────────── v2.0.0 Installed StatsModels ───────────────── v0.6.33 Installed Combinatorics ─────────────── v1.0.3 Installed BioSequences ──────────────── v3.5.0 Installed DifferentiationInterface ──── v0.7.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed Xorg_libXi_jll ────────────── v1.8.3+0 Installed SIMD ──────────────────────── v3.7.1 Installed Wayland_jll ───────────────── v1.24.0+0 Installed Colors ────────────────────── v0.13.1 Installed GtkObservables ────────────── v2.2.0 Installed Twiddle ───────────────────── v1.1.2 Installed Xorg_libxkbfile_jll ───────── v1.1.3+0 Installed StaticArraysCore ──────────── v1.4.3 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed StaticArrays ──────────────── v1.9.14 Installed MathOptInterface ──────────── v1.42.1 Installed Xorg_xkbcomp_jll ──────────── v1.4.7+0 Installed Documenter ────────────────── v0.27.25 Installed ColorTypes ────────────────── v0.12.1 Installed Glib_jll ──────────────────── v2.84.3+0 Installed Requires ──────────────────── v1.3.1 Installed StringManipulation ────────── v0.4.1 Installed Git_jll ───────────────────── v2.50.1+0 Installed DiffRules ─────────────────── v1.15.1 Installed LogExpFunctions ───────────── v0.3.29 Installed JSON ──────────────────────── v0.21.4 Installed Parsers ───────────────────── v2.8.3 Installed PrettyTables ──────────────── v2.4.0 Installed Distributions ─────────────── v0.25.120 Installed Rmath ─────────────────────── v0.8.0 Installed FiniteDiff ────────────────── v2.27.0 Installed StatsFuns ─────────────────── v1.5.0 Installed BioGenerics ───────────────── v0.1.5 Installed DocumenterTools ───────────── v0.1.20 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed Xorg_xkeyboard_config_jll ─── v2.44.0+0 Installed DataFrames ────────────────── v1.7.0 Installed WeakRefStrings ────────────── v1.4.2 Installed XZ_jll ────────────────────── v5.8.1+0 Installed JLLWrappers ───────────────── v1.7.1 Installed MutableArithmetics ────────── v1.6.4 Installed Pango_jll ─────────────────── v1.56.3+0 Installed StructTypes ───────────────── v1.11.0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed JpegTurbo_jll ─────────────── v3.1.1+0 Installed NLopt ─────────────────────── v0.6.5 Installed FilePathsBase ─────────────── v0.9.24 Installed GLM ───────────────────────── v1.8.3 Installed FlameGraphs ───────────────── v1.1.0 Installed ConstructionBase ──────────── v1.6.0 Installed Adapt ─────────────────────── v4.3.0 Installed Libmount_jll ──────────────── v2.41.0+0 Installed HypergeometricFunctions ───── v0.3.28 Installed PhyloNetworks ─────────────── v0.15.3 Installed Gumbo_jll ─────────────────── v0.10.2+0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Compat ────────────────────── v4.18.0 Installed Statistics ────────────────── v1.11.1 Installed TranscodingStreams ────────── v0.11.3 Installed Suppressor ────────────────── v0.2.8 Installed PositiveFactorizations ────── v0.2.4 Installed StatsAPI ──────────────────── v1.7.1 Installed PrecompileTools ───────────── v1.3.2 Installed Libepoxy_jll ──────────────── v1.5.11+0 Installed xkbcommon_jll ─────────────── v1.9.2+0 Installed CodecBzip2 ────────────────── v0.8.5 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed JSON3 ─────────────────────── v1.14.3 Installed BioSymbols ────────────────── v5.2.0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed ProfileView ───────────────── v1.10.1 Installed hicolor_icon_theme_jll ────── v0.18.0+0 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Parameters ────────────────── v0.12.3 Installed XML2_jll ──────────────────── v2.13.6+1 Installed PtrArrays ─────────────────── v1.3.0 Installed iso_codes_jll ─────────────── v4.17.0+0 Installed IntervalSets ──────────────── v0.7.11 Installed SpecialFunctions ──────────── v2.5.1 Installed FixedPointNumbers ─────────── v0.8.5 Installed gdk_pixbuf_jll ────────────── v2.42.13+0 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Git ───────────────────────── v1.4.0 Installed Gumbo ─────────────────────── v0.8.3 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed PhyNEST ───────────────────── v0.1.12 Installed LineSearches ──────────────── v7.4.0 Installed IndirectArrays ────────────── v1.0.0 Installed Xorg_libXrandr_jll ────────── v1.5.5+0 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Automa ────────────────────── v1.1.0 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed ANSIColoredPrinters ───────── v0.0.1 Installed MathProgBase ──────────────── v0.7.8 Installed CSV ───────────────────────── v0.10.15 Installed Gtk4 ──────────────────────── v0.7.9 Installing 59 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_libXdamage 50.0 KiB Installed artifact Xorg_libXrandr 354.5 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact xkbcommon 263.7 KiB Installed artifact Xorg_libxkbfile 486.7 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact LERC 272.9 KiB Installed artifact Xorg_xkbcomp 274.8 KiB Installed artifact Libtiff 3.2 MiB Installed artifact XZ 1.5 MiB Installed artifact Wayland 390.6 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Cairo 2.2 MiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact adwaita_icon_theme 5.0 MiB Installed artifact Graphene 223.2 KiB Installed artifact Pango 1.1 MiB Installed artifact Libmount 6.4 MiB Installed artifact Xorg_xkeyboard_config 537.5 KiB Installed artifact Rmath 121.9 KiB Installed artifact Gumbo 703.8 KiB Installed artifact Libffi 44.2 KiB Installed artifact Xorg_libXi 1.6 MiB Installed artifact HarfBuzz 1.7 MiB Installed artifact iso_codes 7.0 MiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXinerama 50.1 KiB Installed artifact NLopt 322.7 KiB Installed artifact OpenSSH 4.2 MiB Installed artifact Libiconv 1.9 MiB Installed artifact JpegTurbo 1.6 MiB Installed artifact Bzip2 503.5 KiB Installed artifact Xorg_libXfixes 195.9 KiB Installed artifact Expat 271.4 KiB Installed artifact Xorg_libXcursor 227.1 KiB Installed artifact libpng 328.4 KiB Installed artifact Glib 7.7 MiB Installed artifact Fontconfig 522.5 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Wayland_protocols 185.1 KiB Installed artifact LZO 208.9 KiB Installed artifact XML2 2.5 MiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Libepoxy 504.4 KiB Installed artifact Graphite2 120.2 KiB Installed artifact gdk_pixbuf 943.6 KiB Installed artifact libsass 8.9 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Librsvg 9.3 MiB Installed artifact hicolor_icon_theme 13.2 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Pixman 372.2 KiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact GTK4 14.1 MiB Installed artifact Git 48.8 MiB Updating `~/.julia/environments/v1.13/Project.toml` [115de871] + PhyNEST v0.1.12 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.16.0 [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.19.0 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [d1d4a3ce] + BitFlags v0.1.9 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [861a8166] + Combinatorics v1.0.3 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.18.0 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.4 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.20 [4e289a0a] + EnumX v1.0.5 [c2308a5c] + FASTX v2.1.7 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [08572546] + FlameGraphs v1.1.0 [f6369f11] + ForwardDiff v1.0.1 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [d7ba0133] + Git v1.4.0 [a2bd30eb] + Graphics v1.1.3 [9db2cae5] + Gtk4 v0.7.9 [8710efd8] + GtkObservables v2.2.0 [708ec375] + Gumbo v0.8.3 [34004b35] + HypergeometricFunctions v0.3.28 [b5f81e59] + IOCapture v0.2.5 [9b13fd28] + IndirectArrays v1.0.0 [842dd82b] + InlineStrings v1.4.4 [8197267c] + IntervalSets v0.7.11 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [d3d80556] + LineSearches v7.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.42.1 [fdba3010] + MathProgBase v0.7.8 ⌅ [85b6ec6f] + MethodAnalysis v0.4.13 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.4 [d41bc354] + NLSolversBase v7.10.0 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.3 [510215fc] + Observables v0.5.5 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [115de871] + PhyNEST v0.1.12 ⌅ [33ad39ac] + PhyloNetworks v0.15.3 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [c46f51b8] + ProfileView v1.10.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [d5f540fe] + RoundingIntegers v1.1.0 [fdea26ae] + SIMD v3.7.1 [322a6be2] + Sass v0.2.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3eaba693] + StatsModels v0.6.33 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.5 [856f2bd8] + StructTypes v1.11.0 [fd094767] + Suppressor v0.2.8 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [3a884ed6] + UnPack v1.0.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [6ebb71f1] + GTK4_jll v4.18.6+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [f8c6e375] + Git_jll v2.50.1+0 [7746bdde] + Glib_jll v2.84.3+0 [75302f13] + Graphene_jll v1.10.8+0 [3b182d85] + Graphite2_jll v1.3.15+0 [528830af] + Gumbo_jll v0.10.2+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [42c93a91] + Libepoxy_jll v1.5.11+0 [e9f186c6] + Libffi_jll v3.4.7+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [925c91fb] + Librsvg_jll v2.54.7+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.41.0+0 [079eb43e] + NLopt_jll v2.10.0+0 ⌅ [9bd350c2] + OpenSSH_jll v9.9.2+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [36c8627f] + Pango_jll v1.56.3+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [a2964d1f] + Wayland_jll v1.24.0+0 [2381bf8a] + Wayland_protocols_jll v1.44.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [0aeada51] + Xorg_libXdamage_jll v1.1.6+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.1+0 [a51aa0fd] + Xorg_libXi_jll v1.8.3+0 [d1454406] + Xorg_libXinerama_jll v1.1.6+0 [ec84b674] + Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.1.3+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [b437f822] + adwaita_icon_theme_jll v43.0.1+0 [da03df04] + gdk_pixbuf_jll v2.42.13+0 [059c91fe] + hicolor_icon_theme_jll v0.18.0+0 [bf975903] + iso_codes_jll v4.17.0+0 [b53b4c65] + libpng_jll v1.6.50+0 [47bcb7c8] + libsass_jll v3.6.6+0 [d8fb68d0] + xkbcommon_jll v1.9.2+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 28.93s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4329.7 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 862.98s ################################################################################ # Testing # Testing PhyNEST Status `/tmp/jl_S9Vcgj/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [d3d80556] LineSearches v7.4.0 [429524aa] Optim v1.13.2 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [c46f51b8] ProfileView v1.10.1 ⌅ [2913bbd2] StatsBase v0.33.21 [fd094767] Suppressor v0.2.8 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [56ddb016] Logging v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_S9Vcgj/Manifest.toml` [47edcb42] ADTypes v1.16.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.19.0 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [5ae59095] Colors v0.13.1 [861a8166] Combinatorics v1.0.3 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.0 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.4 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [4e289a0a] EnumX v1.0.5 [c2308a5c] FASTX v2.1.7 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 [08572546] FlameGraphs v1.1.0 [f6369f11] ForwardDiff v1.0.1 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [d7ba0133] Git v1.4.0 [a2bd30eb] Graphics v1.1.3 [9db2cae5] Gtk4 v0.7.9 [8710efd8] GtkObservables v2.2.0 [708ec375] Gumbo v0.8.3 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [9b13fd28] IndirectArrays v1.0.0 [842dd82b] InlineStrings v1.4.4 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [d3d80556] LineSearches v7.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.42.1 [fdba3010] MathProgBase v0.7.8 ⌅ [85b6ec6f] MethodAnalysis v0.4.13 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.4 [d41bc354] NLSolversBase v7.10.0 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.3 [510215fc] Observables v0.5.5 [429524aa] Optim v1.13.2 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [c46f51b8] ProfileView v1.10.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [d5f540fe] RoundingIntegers v1.1.0 [fdea26ae] SIMD v3.7.1 [322a6be2] Sass v0.2.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.14 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 ⌅ [3eaba693] StatsModels v0.6.33 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.5 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [3a884ed6] UnPack v1.0.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.6.5+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [6ebb71f1] GTK4_jll v4.18.6+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [f8c6e375] Git_jll v2.50.1+0 [7746bdde] Glib_jll v2.84.3+0 [75302f13] Graphene_jll v1.10.8+0 [3b182d85] Graphite2_jll v1.3.15+0 [528830af] Gumbo_jll v0.10.2+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [aacddb02] JpegTurbo_jll v3.1.1+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [42c93a91] Libepoxy_jll v1.5.11+0 [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [925c91fb] Librsvg_jll v2.54.7+0 [89763e89] Libtiff_jll v4.7.1+0 [38a345b3] Libuuid_jll v2.41.0+0 [079eb43e] NLopt_jll v2.10.0+0 ⌅ [9bd350c2] OpenSSH_jll v9.9.2+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [36c8627f] Pango_jll v1.56.3+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [a2964d1f] Wayland_jll v1.24.0+0 [2381bf8a] Wayland_protocols_jll v1.44.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [ffd25f8a] XZ_jll v5.8.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [935fb764] Xorg_libXcursor_jll v1.2.4+0 [0aeada51] Xorg_libXdamage_jll v1.1.6+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [d091e8ba] Xorg_libXfixes_jll v6.0.1+0 [a51aa0fd] Xorg_libXi_jll v1.8.3+0 [d1454406] Xorg_libXinerama_jll v1.1.6+0 [ec84b674] Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [cc61e674] Xorg_libxkbfile_jll v1.1.3+0 [35661453] Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b437f822] adwaita_icon_theme_jll v43.0.1+0 [da03df04] gdk_pixbuf_jll v2.42.13+0 [059c91fe] hicolor_icon_theme_jll v0.18.0+0 [bf975903] iso_codes_jll v4.17.0+0 [b53b4c65] libpng_jll v1.6.50+0 [47bcb7c8] libsass_jll v3.6.6+0 [d8fb68d0] xkbcommon_jll v1.9.2+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Test Summary: | Pass Total Time Testing misc.function get_average | 100 100 1.9s Test Summary: | Pass Total Time Testing site pattern proabilities | 1000 1000 0.1s Test Summary: | Pass Total Time Testing Method-of-moment estimates of speciation times | 1500 1500 0.1s Testing PhyNEST tests passed Testing completed after 35.88s PkgEval succeeded after 968.58s